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Giovanni Campagna, a GNOME Shell developer, has reported a bug and already submitted 3 patches for including libappindicator + dbusmenu support in GNOME Shell as a part of the core, not as an extension (because it can't be implemented as an extension).

What does this mean? Well, if this is approved, GNOME Shell will get AppIndicator support so all those cool Ubuntu AppIndicators will work in GNOME Shell (as well as KDE apps that use a tray icon).

The AppIndicators will show up in the GNOME Shell Message Tray (displayed at the bottom of the screen) and they work a bit differently compared to the Ubuntu implementation: clicking the notification brings the application forward (if the AppIndicator isn't a stand-alone app), the menu shows up on right click and they support tooltips, as opposed to Ubuntu. But of course, this may change (again, if this is approved):

This commit adds a tray based on KDE/Ayatana/proposed Freedesktop protocol for renewed tray communication. Icons following this protocol support menus, titles and tooltips, as well as providing status and category, thus allowing seamless integration in the desktop shell. In the Shell, they are rendered as Message Tray sources, with attached a Notification acting as the tooltip. Clicking on the notification brings the application forward, as usual. Next patch will add support for DBusMenu.

- Giovanni Campagna

I've tried compiling the latest GNOME Shell with these patches in Ubuntu 11.10 and the AppIndicators show up, but the right click menu didn't work for me. Here are a couple of screenshots: